title: Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper.
abstract: BACKGROUND
  Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10.
  
  
  RESULTS
  We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity.
  
  
  CONCLUSIONS
  Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.
authors.affiliation: Department of Plant Pathology, University of Florida, Gainesville, FL, USA. jbjones@ufl.edu
authors.forename: Neha
authors.initials: N
authors.lastname: Potnis
authors.forename: Ksenia
authors.initials: K
authors.lastname: Krasileva
authors.forename: Virginia
authors.initials: V
authors.lastname: Chow
authors.forename: Nalvo F
authors.initials: NF
authors.lastname: Almeida
authors.forename: Prabhu B
authors.initials: PB
authors.lastname: Patil
authors.forename: Robert P
authors.initials: RP
authors.lastname: Ryan
authors.forename: Molly
authors.initials: M
authors.lastname: Sharlach
authors.forename: Franklin
authors.initials: F
authors.lastname: Behlau
authors.forename: J Max
authors.initials: JM
authors.lastname: Dow
authors.forename: Mt
authors.initials: M
authors.lastname: Momol
authors.forename: Frank F
authors.initials: FF
authors.lastname: White
authors.forename: James F
authors.initials: JF
authors.lastname: Preston
authors.forename: Boris A
authors.initials: BA
authors.lastname: Vinatzer
authors.forename: Ralf
authors.initials: R
authors.lastname: Koebnik
authors.forename: João C
authors.initials: JC
authors.lastname: Setubal
authors.forename: David J
authors.initials: DJ
authors.lastname: Norman
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Staskawicz
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Jones
mesh_terms: D058947:Bacterial Secretion Systems / Q000235:genetics; D002212:Capsicum / Q000382:microbiology*; D055028:Comparative Genomic Hybridization; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D005810:Multigene Family; D010802:Phylogeny; D010935:Plant Diseases / Q000382:microbiology; D017422:Sequence Analysis, DNA; D014974:Xanthomonas / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D058947:Bacterial Secretion Systems; D004269:DNA, Bacterial